Rapid detection of biological warfare agents (BWA) in field is critical to provide appropriate countermeasures to deployment of weapons of mass destruction. The first responders in the field need instruments which will be portable (less than 10 kg), provide specific detection of a number of pathogens (desirable 810), with analysis time of ca 1-2 hours and which will not require special skills for their operation. There are numerous analyzers available for detection of pathogens in liquid samples, however, a major obstacle for their efficient use in the field is that they do not integrate sample preparation with the detection system. The methods based on analyzing DNA characteristic for each pathogen in the sample have been shown to provide most specific response and can be used when detection of multiple agents is needed. Analysis of nucleic acids requires a series of analytical steps which are difficult to integrate and automate in a field portable instrument. A unique microfluidic system is proposed which integrates pathogen separation from complex liquid samples, pathogen lysis, amplification of DNA and detection. Nanogen's commercially available electronic chip array for electrophoretic accumulation of DNA and fluoroprobes and for detection of DNA will be modified to include sample preparation step. A disposable DNA chip array will be developed with integrated sample preparation steps. The proposed method builds on developed technology and on incorporation of several innovations which will assure a quick development of a new portable field detector for detection of multiple biological agents and will be very flexible to accommodate other or new types of analytes.